The overall focus of this proposal is a detailed study of the within-host population dynamics for a retrovirus vaccine. It will synthesize both empirical studies of the genetic diversity, sequence divergence, and phylogenetic relationships of these sequences, derived from various anatomic compartments and at various times post-infection, and theoretical studies that determine the nature of viral population structure within an infected host. To complement the sequence analyses in the empirical studies, we will test for the presence of replication-competent virus genomes present in different compartments as well as examine the laboratory and clinical signs of development of immunodeficiency. The empirical studies will seek to determine the extent to which viral replication and movement is associated with specific cell types or organ systems. The theoretical component of our proposed research will examine the consequences of such structure for both viral dynamics and evolution. The use of this macaque model has significant advantages over human studies in that we can infect macaques with the molecular clone of vaccine Dvpu SHIVPPC, allowing for unambiguous evidence of virus evolution in vivo . These types of investigations are necessary preliminary studies before any attempt to use live HIV-related vaccines in human HIV-1 patients. The evolutionary relationships of the vaccine genomes will be examined at early times post-infection in young rhesus macaques post-vaccination, specifically the genetic diversity, sequence divergence present in various sites (plasma, PMBCs, brain, lymph nodes, thymus, gut-associated lymphoid tissues, spleen, kidney, tonsils, bone marrow) and phylogenetic relationships of vaccine virus sequences from these tissues at necropsies. In additional animals held for several months to 5 years, longitudinal data will be derived by obtaining sequence information from up to 3 spleen biopsies and monthly lymph node biopsies, plasma, cerebrospinal fluid (CSF), and peripheral blood mononuclear cell (PBMC) samples. Sequence data will be analyzed to determine if sequences from any time point or anatomic compartment share more genetic identity with each other than to sequences from other compartments or timepoints. Additionally, a similar procedure will be used to examine the temporal structure in each compartment. The theoretical studies will explore the dynamical consequences of population structure arising from within-host heterogeneity and spatial flows, developing the theory recursively, via continuous modification and updating of our basic models utilizing the results from the experimental parts of the proposal.